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- PDB-2mjk: Nmr structure of hen egg beta-defensin gallin (chicken ovo-defensin) -

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Basic information

Entry
Database: PDB / ID: 2mjk
TitleNmr structure of hen egg beta-defensin gallin (chicken ovo-defensin)
ComponentsGallin protein
KeywordsANTIMICROBIAL PROTEIN
Function / homologyMeleagrin/Cygnin / Meleagrin/Cygnin family / Antimicrobial Peptide, Beta-defensin 2; Chain A / Antimicrobial Peptide, Beta-defensin 2; Chain A / Roll / Alpha Beta / Gallin protein
Function and homology information
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model1
AuthorsLandon, C. / Meudal, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Three-dimensional NMR Structure of Hen Egg Gallin (Chicken Ovodefensin) Reveals a New Variation of the beta-Defensin Fold.
Authors: Herve, V. / Meudal, H. / Labas, V. / Rehault-Godbert, S. / Gautron, J. / Berges, M. / Guyot, N. / Delmas, A.F. / Nys, Y. / Landon, C.
History
DepositionJan 10, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gallin protein


Theoretical massNumber of molelcules
Total (without water)4,7391
Polymers4,7391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Gallin protein


Mass: 4738.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Gallus gallus (chicken) / References: UniProt: D5GR55
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D DQF-COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY
1712D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM GALLIN PROTEIN, 90% H2O/10% D2O90% H2O/10% D2O
21 mM GALLIN PROTEIN, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMGALLIN PROTEIN-11
1 mMGALLIN PROTEIN-22
Sample conditionsIonic strength: 0 / pH: 5.5 / Pressure: AMBIENT / Temperature: 293 K

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NMR measurement

NMR spectrometerType: VARIAN INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIA1.1LINGE, O'DONOGHUErefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRViewJohnson, One Moon Scientificstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: EXPLICIT WATER
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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